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This page was generated on 2024-06-18 17:58 -0400 (Tue, 18 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4758
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4492
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4464
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4464
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 825/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomAutomorphism 1.6.0  (landing page)
Robersy Sanchez
Snapshot Date: 2024-06-16 14:00 -0400 (Sun, 16 Jun 2024)
git_url: https://git.bioconductor.org/packages/GenomAutomorphism
git_branch: RELEASE_3_19
git_last_commit: 22d7b7a
git_last_commit_date: 2024-04-30 11:43:53 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    ERROR    OK  


CHECK results for GenomAutomorphism on palomino3

To the developers/maintainers of the GenomAutomorphism package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenomAutomorphism.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: GenomAutomorphism
Version: 1.6.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GenomAutomorphism.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings GenomAutomorphism_1.6.0.tar.gz
StartedAt: 2024-06-17 04:14:28 -0400 (Mon, 17 Jun 2024)
EndedAt: 2024-06-17 04:23:26 -0400 (Mon, 17 Jun 2024)
EllapsedTime: 538.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: GenomAutomorphism.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GenomAutomorphism.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings GenomAutomorphism_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/GenomAutomorphism.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'GenomAutomorphism/DESCRIPTION' ... OK
* this is package 'GenomAutomorphism' version '1.6.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'GenomAutomorphism' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'AutomorphismList,ANY'
  generic '[' and siglist 'ListCodonMatrix,ANY'
  generic '[' and siglist 'MatrixSeq,ANY'
  generic '[[' and siglist 'AutomorphismList'
  generic '[[' and siglist 'ListCodonMatrix'
  generic 'names<-' and siglist 'AutomorphismList'
  generic 'names<-' and siglist 'MatrixSeq'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
aminoacid_dist    3.69   0.36  112.67
codon_dist_matrix 0.05   0.01   10.60
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'spelling.R'
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING
See
  'F:/biocbuild/bbs-3.19-bioc/meat/GenomAutomorphism.Rcheck/00check.log'
for details.


Installation output

GenomAutomorphism.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL GenomAutomorphism
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'GenomAutomorphism' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GenomAutomorphism)

Tests output

GenomAutomorphism.Rcheck/tests/spelling.Rout


R version 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> if (requireNamespace("spelling", quietly = TRUE)) {
+     spelling::spell_check_test(
+         vignettes = TRUE, error = FALSE,
+         skip_on_cran = TRUE
+     )
+ }
NULL
> 
> proc.time()
   user  system elapsed 
   0.18    1.40    1.48 

GenomAutomorphism.Rcheck/tests/testthat.Rout


R version 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(GenomAutomorphism)
> 
> test_check("GenomAutomorphism")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 33 ]
> 
> proc.time()
   user  system elapsed 
  20.62    9.75   69.14 

Example timings

GenomAutomorphism.Rcheck/GenomAutomorphism-Ex.timings

nameusersystemelapsed
AutomorphismByCoef0.370.020.39
AutomorphismList2.220.342.56
CodonMatrix0.210.000.20
CodonSeq0.530.581.11
GRangesMatrixSeq0.110.130.23
ListCodonMatrix0.320.000.33
MatrixSeq0.150.010.16
aa_phychem_index0.070.030.11
aaindex10.050.000.04
aaindex20.020.020.04
aaindex30.000.010.01
aln0.200.290.49
aminoacid_dist 3.69 0.36112.67
as.AutomorphismList0.620.020.64
aut3D1.240.311.55
autZ1252.480.302.78
autZ50.580.310.89
autZ641.390.261.67
autby_coef0.230.020.25
autm0.180.260.44
autm_3d0.090.110.20
autm_z1250.160.480.66
automorphismByRanges0.200.320.51
automorphism_bycoef0.170.290.47
automorphisms3.630.323.93
base2codon0.210.200.43
base2int000
base_methods0.440.340.78
brca1_aln0.060.000.07
brca1_aln20.100.000.09
brca1_autm0.300.020.32
cdm_z640.380.220.61
codon_coord1.090.391.48
codon_dist0.610.611.22
codon_dist_matrix 0.05 0.0110.60
codon_matrix0.580.030.61
conserved_regions0.440.771.21
covid_aln0.140.270.40
covid_autm0.140.460.61
cyc_aln0.140.320.46
cyc_autm0.240.370.61
dna_phyche0.000.020.02
dna_phychem000
extract-methods0.390.030.42
getAutomorphisms0.230.330.56
get_coord0.580.280.88
get_mutscore0.140.030.17
matrices0.520.340.86
mod000
modeq000
modlineq000
mut_type000
peptide_phychem_index0.090.050.14
reexports0.240.590.83
seqranges0.570.300.87
slapply000
sortByChromAndStart0.060.000.06
str2chr000
str2dig000
translation1.080.551.62